aibiology

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SAM文件flags解释

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SAM flag

SAM文件是二进制比对文件，其中FLAG值记录了该read的比对信息。 FLAG巧妙地采用二进制来存储信息，解读FLAG即可确定read属性，所以samtools常常依据FLAG来过滤处理SAM/BAM。

Python code

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import argparse

def parse_args():
    parser = argparse.ArgumentParser()
    parser.add_argument('-i', '--input', type=int, required=True,
                           help='flags in SAM')
    return parser.parse_args()


def flags_cal(flag: int):
    falgs = [0x1, 0x2, 0x4, 0x8, 0x10, 0x20, 0x40, 0x80, 0x100, 0x200, 0x400, 0x800]
    flags_dict = {
        0x1: ['PAIRED', '..paired-end (or multiple-segment) sequencing technology'],
        0x2: ['PROPER_PAIR', '..each segment properly aligned according to the aligner'],
        0x4: ['UNMAP', '..segment unmapped'],
        0x8: ['MUNMAP', '..next segment in the template unmapped'],
        0x10: ['REVERSE', '..SEQ is reverse complemented'],
        0x20: ['MREVERSE', '..SEQ of the next segment in the template is reversed'],
        0x40: ['READ1', '..the first segment in the template'],
        0x80: ['READ2', '..the last segment in the template'],
        0x100: ['SECONDARY', '..secondary alignment'],
        0x200: ['QCFAIL', '..not passing quality controls'],
        0x400: ['DUPLICATE', '..PCR or optical duplicate'],
        0x800: ['SUPPLEMENTARY', '..supplementary alignment']
        }
    binary = bin(flag)
    index_falgs = list(map(int, list(binary[2:][::-1])))
    index_list = []
    hex_list = []
    print()
    print(f'Flags: {flag}')
    print()
    print("Hex\tDec\tProperty\tInformation") 
    Props = []
    for index,i in enumerate(index_falgs):
        if i == 1:
            index_list.append(index_list)
            hexs = falgs[index]
            ints = int(hexs)
            info = flags_dict[hexs]
            Props.append(info[0])
            print("{:<#x}\t{:<5d}\t{:<11s}\t{:<50s}".format(hexs, ints, info[0], info[1]))
            # print("%#x %s %s %s "%(hexs, hexs, info[0], info[1]))
    print()
    print("{}\t{:<5d}\t{}".format(hex(flag), flag, ",".join(Props)))


if __name__ == '__main__':
    args = parse_args()
    flags_cal(args.input)

执行程序即可解析 

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$ python flags_explain.py -i 1294 
Flags: 1294

Hex	Dec	Property	Information
0x2	2    	PROPER_PAIR	..each segment properly aligned according to the aligner
0x4	4    	UNMAP      	..segment unmapped                                
0x8	8    	MUNMAP     	..next segment in the template unmapped           
0x100	256  	SECONDARY  	..secondary alignment                             
0x400	1024 	DUPLICATE  	..PCR or optical duplicate                        

0x50e	1294 	PROPER_PAIR,UNMAP,MUNMAP,SECONDARY,DUPLICATE

## htslib

htslib 

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/*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
#define BAM_FPAIRED        1
/*! @abstract the read is mapped in a proper pair */
#define BAM_FPROPER_PAIR   2
/*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
#define BAM_FUNMAP         4
/*! @abstract the mate is unmapped */
#define BAM_FMUNMAP        8
/*! @abstract the read is mapped to the reverse strand */
#define BAM_FREVERSE      16
/*! @abstract the mate is mapped to the reverse strand */
#define BAM_FMREVERSE     32
/*! @abstract this is read1 */
#define BAM_FREAD1        64
/*! @abstract this is read2 */
#define BAM_FREAD2       128
/*! @abstract not primary alignment */
#define BAM_FSECONDARY   256
/*! @abstract QC failure */
#define BAM_FQCFAIL      512
/*! @abstract optical or PCR duplicate */
#define BAM_FDUP        1024
/*! @abstract supplementary alignment */
#define BAM_FSUPPLEMENTARY 2048